Michael,
A Masters is potentially a program that can teach you a broad set of skills including how to think critically, how to communicate effectively, how to teach yourself, and how to work with others.
A certificate is going to teach you how to do a specific set of tasks in a certain domain (i.e. Window Server management).
The thing with certificates is that they last for no more than 10 years and typically only 5. In addition, some people view certificates as an anti-credential and count them against the candidate with the theory that certificates aren't demonstrative of true comprehension of the subject matter.
I would choose the Masters since it's a credential that lasts a lifetime but of course it's also far more expensive that just a series of certs.
Cheers,
Adam